3IB0

Structural basis of the prevention of NSAID-induced damage of the gastrointestinal tract by C-terminal half (C-lobe) of bovine colostrum protein lactoferrin: Binding and structural studies of C-lobe complex with diclofenac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 3IB0

Classification: METAL BINDING PROTEIN

Total Structure Weight: 41024.86

Macromolecule Entities
Molecule Chains Length Organism Details
Lactotransferrin A 345 Bos taurus EC#: 3.4.21 IUBMB
Fragment: UNP residues 361-705
Mutation: N565K, K608E
Gene Name(s): LTF Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DIF
Query on DIF

A 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID
DICLOFENAC (Synonym)
C14 H11 Cl2 N O2
DCOPUUMXTXDBNB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CO3
Query on CO3

A CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EOH
Query on EOH

A ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.193
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 61.43 α = 90.00
b = 49.87 β = 107.10
c = 65.17 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2009-07-15
  • Released Date: 2009-08-11
  • Deposition author(s): Mir, R., Singh, N., Sinha, M., Sharma, S., Kaur, P., Srinivasan, A., Singh, T.P.
  • This entry supercedes: 2B6D 3HWV

Revision History

  • Version 1_0: 2009-08-11

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_2: 2018-08-01

    Type: Data collection, Database references, Source and taxonomy, Structure summary

  • Version 1_3: 2018-08-15

    Type: Data collection, Database references, Source and taxonomy, Structure summary